Search for Variation information by Variation ID:
Detailed information for vg0327370671:
| Variant ID: vg0327370671 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 27370671 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACCGGCGAGCGCGCGGCGAGCACGGCGCGGTGTGCATGAAACGTCTCGCTGCCGACGGAGAACAACACGTCCGAGCCGTCGGCACGGTCCGCGATGTCGT[C/T]
GAGCTGGCCGTTGAGGTTCGACCGCGGGATGGGTATAGTGCCGTCGTCATCACCGGCATATAATATATATTTAAGAAAAGTAAAAATAGGGGGAAACAGT
Reverse complement sequence
ACTGTTTCCCCCTATTTTTACTTTTCTTAAATATATATTATATGCCGGTGATGACGACGGCACTATACCCATCCCGCGGTCGAACCTCAACGGCCAGCTC[G/A]
ACGACATCGCGGACCGTGCCGACGGCTCGGACGTGTTGTTCTCCGTCGGCAGCGAGACGTTTCATGCACACCGCGCCGTGCTCGCCGCGCGCTCGCCGGT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 65.30% | 34.40% | 0.17% | 0.06% | NA |
| All Indica | 2759 | 97.90% | 1.80% | 0.18% | 0.07% | NA |
| All Japonica | 1512 | 1.30% | 98.50% | 0.13% | 0.07% | NA |
| Aus | 269 | 97.00% | 3.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.00% | 0.80% | 0.17% | 0.00% | NA |
| Indica II | 465 | 98.50% | 1.10% | 0.00% | 0.43% | NA |
| Indica III | 913 | 97.40% | 2.40% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 97.50% | 2.30% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 0.70% | 99.10% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 1.80% | 98.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.50% | 97.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 52.10% | 47.90% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 60.00% | 38.90% | 1.11% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0327370671 | C -> T | LOC_Os03g48120.1 | missense_variant ; p.Asp41Asn; MODERATE | nonsynonymous_codon ; D41N | Average:77.369; most accessible tissue: Zhenshan97 panicle, score: 87.764 | benign  |
0.098 |
TOLERATED | 0.06 |
| vg0327370671 | C -> DEL | LOC_Os03g48120.1 | N | frameshift_variant | Average:77.369; most accessible tissue: Zhenshan97 panicle, score: 87.764 | N | N | N | N |